xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-03 02:18:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r721

Browse Source
This commit is contained in:
chhylp123
2025-03-14 01:40:21 -04:00
parent a96191560e
commit b3b18ab1d0
4 changed files with 246 additions and 29 deletions
Download Patch File Download Diff File Expand all files Collapse all files
ecovlp.cpp
+140 -9
View File
@@ -65,6 +65,12 @@ typedef struct {
uint8_t *cr;
} ec_ovec_buf_t;
typedef struct {
ec_ovec_buf_t *p;
asg64_v idx;
ma_ug_t *ug;
} ec_polish_buf_t;
typedef struct {
uint32_t n_thread, n_a, chunk_size, cn;
FILE *fp;
@@ -2801,7 +2807,7 @@ inline uint64_t exact_ec_check(char *qstr, uint64_t ql, char *tstr, uint64_t tl,
return 0;
}
void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v *buf, asg64_v *srt, ma_hit_t_alloc *in, uint8_t chem_drop)
void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *rref, UC_Read* qu, UC_Read* tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t wl, int64_t rid, int64_t khit, int64_t move_gap, asg16_v *buf, asg64_v *srt, ma_hit_t_alloc *in, uint8_t chem_drop, double align_gap_rate, int64_t align_gap_max)
{
if(ol->length <= 0) return;
@@ -2817,7 +2823,7 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
}
if(!(srt->n)) {
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop);
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max);
} else {
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
@@ -2852,9 +2858,10 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
if(on > nec) {
gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop);
gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max);
}
// fprintf(stderr, "[M::%s] srt->n::%u, nec::%lu, on::%lu\n", __func__, (uint32_t)srt->n, nec, on);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
}
@@ -3257,6 +3264,8 @@ static void worker_hap_ec(void *data, long i, int tid)
///for debug indel
// if(i != 1238) return;
// if(i != 2410) return;
// if(i != 4198005) return;
// if(i != 682) return;
// debug_retrive_bqual(D, &b->v8t, i, 256); return;
@@ -3276,7 +3285,7 @@ static void worker_hap_ec(void *data, long i, int tid)
///mz1_ha_sketch(rs, rl, mz_w, mz_k, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 0, NULL);
// if((asm_opt.is_ont) && (b->olist.length)) get_mz1(qu->seq, qu->length, RES_W, RES_K, 0, !(asm_opt.flag & HA_F_NO_HPC), b->ab, NULL, NULL, asm_opt.mz_sample_dist, NULL, NULL, NULL, -1, asm_opt.dp_min_len, -1, &(b->sp), asm_opt.mz_rewin, 0, NULL, 0);
gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT/**asm_opt.k_mer_length**/, 1, &b->v16, &b->v64, &(R_INF.paf[i]), asm_opt.is_ont);
gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT/**asm_opt.k_mer_length**/, 1, &b->v16, &b->v64, &(R_INF.paf[i]), asm_opt.is_ont, (asm_opt.is_ont)?(0.006):(-1), (asm_opt.is_ont)?(64):(-1));
///for debug indel
// prt_ovlp_sam(&b->olist, &b->ovlp_read, b->self_read.seq, b->self_read.length);
@@ -3404,7 +3413,7 @@ static void worker_hap_ec_dbg_paf(void *data, long i, int tid)
aux_o = fetch_aux_ovlp(&b->olist);///must be here
// stderr_phase_ovlp(&b->olist);
gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT, 1, &b->v16, &b->v64, &(R_INF.paf[i]), 0);
gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT, 1, &b->v16, &b->v64, &(R_INF.paf[i]), 0, -1, -1);
uint32_t k, m, tl; overlap_region *z; bit_extz_t ez; ma_hit_t *t;
for (k = 0; k < b->olist.length; k++) {
@@ -3796,6 +3805,42 @@ static void worker_hap_dc_ec(void *data, long i, int tid)
refresh_ec_ovec_buf_t0(b, REFRESH_N);
}
static void worker_update_dc_ec(void *data, long i, int tid)
{
ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[tid]);
uint64_t k; ma_hit_t *z;
// fprintf(stderr, "-0-[M::%s-beg] rid->%ld\n", __func__, i);
// if (memcmp("m64012_190921_234837/139067658/ccs", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
// fprintf(stderr, "-0-[M::%s-beg] rid->%ld\n", __func__, i);
// } else if (memcmp("m64012_190921_234837/28968323/ccs", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
// fprintf(stderr, "-1-[M::%s-beg] rid->%ld\n", __func__, i);
// } else {
// return;
// }
// if(i != 2851) return;
// if(scb.a[i].m < scc.a[i].n) {
// scb.a[i].m = scc.a[i].n;
// REALLOC(scb.a[i].a, scb.a[i].m);
// }
// scb.a[i].n = scc.a[i].n;
// memcpy(scb.a[i].a, scc.a[i].a, scc.a[i].n*sizeof((*(scb.a[i].a))));
if(!(R_INF.paf[i].length)) return;
recover_UC_Read(&b->self_read, &R_INF, i);
for (k = 0; k < R_INF.paf[i].length; k++) {
z = &(R_INF.paf[i].buffer[k]);
if((z->el) && (quick_exact_match(z, &R_INF, &b->self_read, &b->ovlp_read, &scc))) {
z->el = 1; b->cnt[0]++;
} else {
z->el = 0; b->cnt[1]++;
}
}
refresh_ec_ovec_buf_t0(b, REFRESH_N);
}
void flip_paf_rc(uint64_t rid, ma_hit_t_alloc *paf, All_reads *rref)
{
@@ -4280,6 +4325,52 @@ static void worker_hap_dc_ec_chemical_arc_mark(void *data, long i, int tid)
refresh_ec_ovec_buf_t0(b, REFRESH_N);
}
uint64_t get_candidate_rrs(ma_utg_t *u, uint64_t rz)
{
// uint64_t rid, rs, re, rev, k, l[2], lr, ts, te;
// ma_hit_t_alloc *z = NULL;
// ma_hit_t *h = NULL;
// rid = u->a[rz]>>33; rev = (u->a[rz]>>32)&1;
// rs = 0; re = (uint32_t)u->a[rz];
// if(!rev) {
// rs = Get_READ_LENGTH(R_INF, rid) - ((uint32_t)u->a[rz]);
// re = Get_READ_LENGTH(R_INF, rid);
// }
// for (k = lr = 0; k < rz; k++) lr += (uint32_t)u->a[k];
// ts = lr; te = lr + (uint32_t)u->a[k];
// z = &(sources[rid]);
// for (k = 0; k < z->length; k++) {
// h = &(z->buffer[k]);
// if ((Get_qs(*h) <= rs) && (Get_qe(*h) >= re)) {
// l[0] = l[1] = 0;
// if(!(h->rev&rev)) {
// l[0] = Get_ts(*h); l[1] = Get_READ_LENGTH(R_INF, Get_tn(*h)) - Get_te(*h);
// } else {
// l[1] = Get_ts(*h); l[0] = Get_READ_LENGTH(R_INF, Get_tn(*h)) - Get_te(*h);
// }
// }
// }
return 1;
}
static void worker_ec_polish(void *data, long i, int tid)
{
ec_ovec_buf_t0 *b = &(((ec_polish_buf_t*)data)->p->a[tid]);
uint64_t *idx = &(((ec_polish_buf_t*)data)->idx.a[i]);
if(get_candidate_rrs(&(((ec_polish_buf_t*)data)->ug->u.a[(*idx)>>32]), (uint32_t)(*idx))) {
*idx = (uint64_t)-1;
}
refresh_ec_ovec_buf_t0(b, REFRESH_N);
}
void gen_ovlst_paf(ma_hit_t_alloc *in_e, ma_hit_t_alloc *in_r, asg64_v *ou)
{
uint32_t n = 0, k;
@@ -4482,7 +4573,7 @@ overlap_region* h_ec_lchain_re1(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Rea
// fprintf(stderr, "-0-[M::%s]\n", __func__);
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf, 0); rs = qu->seq;
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf, 0, -1, -1); rs = qu->seq;
// fprintf(stderr, "-1-[M::%s]\n", __func__);
@@ -5151,7 +5242,7 @@ overlap_region* h_ec_lchain_re3(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Rea
// fprintf(stderr, "-0-[M::%s]\n", __func__);
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf, 0); rs = qu->seq;
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, asm_opt.max_ov_diff_ec, w.window_length, rid, E_KHIT, 1, buf, 0, -1, -1); rs = qu->seq;
// fprintf(stderr, "-1-[M::%s]\n", __func__);
@@ -6001,6 +6092,22 @@ uint64_t cal_ec_multiple(ec_ovec_buf_t *b, uint64_t n_thre, uint64_t n_a, uint64
return num_correct;
}
void cal_update_ec_multiple(ec_ovec_buf_t *b, uint64_t n_thre, uint64_t n_a)
{
double tt0 = yak_realtime_0();
uint64_t k, num_ec_o = 0, num_nec_o = 0;
for (k = 0; k < n_thre; ++k) b->a[k].cnt[0] = b->a[k].cnt[1] = 0;
kt_for(n_thre, worker_update_dc_ec, b, n_a);///debug_for_fix
for (k = 0; k < n_thre; ++k) {
num_ec_o += b->a[k].cnt[0]; num_nec_o += b->a[k].cnt[1];
}
fprintf(stderr, "[M::pec::%.3f] # exact o: %lu; # non-exact o: %lu\n", yak_realtime_0()-tt0, num_ec_o, num_nec_o);
}
void ha_print_ovlp_stat_1(ec_ovec_buf_t *b, uint64_t n_thre, uint64_t n_a)
{
@@ -6162,7 +6269,7 @@ void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, u
{
// write_ec_reads("ec0.fa");
fprintf(stderr, "[M::%s]\tn_thre::%lu, round::%lu, n_round::%lu, n_a::%lu, is_sv::%lu\n", __func__, n_thre, round, n_round, n_a, is_sv);
// fprintf(stderr, "[M::%s]\tn_thre::%lu, round::%lu, n_round::%lu, n_a::%lu, is_sv::%lu\n", __func__, n_thre, round, n_round, n_a, is_sv);
ec_ovec_buf_t *b = NULL; uint64_t k, is_cr = (round&1);
(*tot_b) = (*tot_e) = 0;
@@ -6177,7 +6284,10 @@ void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, u
sl_ec_r(n_thre, n_a);
}
if(is_sv) kt_for(n_thre, worker_hap_dc_ec, b, n_a);///update overlaps
cal_update_ec_multiple(b, n_thre, n_a);///update overlaps
// if(is_sv) kt_for(n_thre, worker_hap_dc_ec, b, n_a);///update overlaps
if((!is_sv) || (is_sv && is_cr)) {
kt_for(n_thre, worker_hap_post_rev, b, n_a);
@@ -6379,4 +6489,25 @@ uint8_t* gen_chemical_arc_rf(uint64_t n_thre, uint64_t n_a)
b->cr = NULL; destroy_ec_ovec_buf_t(b);
return ra;
}
void gen_hc_polish(uint64_t n_thre, ma_ug_t *ug)
{
ec_polish_buf_t b; memset(&b, 0, sizeof(b)); b.ug = ug;
uint64_t k, z, zn;
for (k = b.idx.n = 0; k < ug->u.n; k++) {
b.idx.n += ug->u.a[k].n;
}
MALLOC(b.idx.a, b.idx.n);
for (k = zn = 0; k < ug->u.n; k++) {
for (z = 0; z < ug->u.a[k].n; z++, zn++) {
b.idx.a[zn] = (k<<32)|z;
}
}
b.p = gen_ec_ovec_buf_t(n_thre);
kt_for(n_thre, worker_ec_polish, &b, b.idx.n);
destroy_ec_ovec_buf_t(b.p); free(b.idx.a);
}